Dials

* _xia2.report_:
* use merged intensities for calculating second moment statistics
* include xtriage report;
* include analysis of distribution of multiplicity in reciprocal space
* add plots of completeness and multiplicity vs resolution
* optionally choose _cc_half_method=sigma_tau_
* _xia2.multi_crystal_analysis_: add stereographic projection plots for crystal orientation analysis
* _xia2.ispyb_xml_: fix for HDF5 files

- fix incorrect anomalous completeness statistics
- bug fix for _pipeline=dials scaler=xdsa_ combination
- putative bug fix for resetting refiners when combined with multi-sweep indexing
- fix for _integrate_p1=True reintegrate_correct_lattice=False_ when lattices are eliminated

- Fix image epoch crashes (xia2/xia290)
- Make HTML reports more responsive (xia2/xia298)

- Fix xia2 html report for sweeps containing a number of images that is not a multiple of 60
- Fix to correctly apply reindexing operations
- Observe _d_min_ and _d_max_ parameters when running in small molecule mode

- Resolution cut-off was too conservative (https://github.com/xia2/xia2/pull/89/commits/45df7e4d37d96b6a2cb5af12fe2ecd10d8174799)
- Updated cctbx loggraph parser to run with new versions of AIMLESS (https://github.com/dials/cctbx/pull/1/commits/7bf85403e0119e7469ea223fbfd5f70b6f934186)
- Various smaller bug fixes (https://github.com/xia2/xia2/pull/89)

- _xia2 -quick_ is now faster & deprecated (use _fast_mode=true_)
- _xia2.cif_ and _.mmcif_ now land in _DataFiles_ directory and contain more entries (xia2/xia266, xia2/xia267, xia2/xia269) including those from the new dxtbx detector database (xia2/xia278)
- When run in small molecule mode (_xia2.small_molecule_ or _small_molecule=True_) SHELXT input files are generated in _DataFiles_ (xia2/xia262)
- absorption surface map and merging statistics table are generated in the _LogFiles_ directory (xia2/xia263, xia2/xia274)
- New parameter _xds.correct.air_ to override the _AIR=_ parameter in XDS correct step
- New parameter _xds.defpix.value_range_for_trusted_detector_pixels_
- _pipeline=dials_: now runs scan-static refinement before scan-varying refinement
- _pipeline=dials_: support index.method=auto
- _pipeline=dials_: optional scaling with XSCALE (_scaler=xdsa_)
- Add ability to override experimental geometry on the command line (xia2/xia287)
- Support for dynamic goniometer shadow masking in DIALS and XDS pipelines (_dynamic_shadowing=True_)
- _xia2.report_ now plots _cc1/2_ and _cc_anom_ critical values